Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development.The HIV 2 glycoprotein is initially expressed as the precursor protein gp160, which is post-translationally cleaved into two non-covalently associated proteins: gp120, the receptor-binding protein that targets the CD4 receptor, and gp41, which mediates the fusion of the viral and host cellular membranes (1, 2). The native, prefusion form of the gp120-gp41 complex is thought to be a trimer comprising three gp120 subunits and three membrane-anchored gp41 subunits and is in a metastable conformation with the heavily glycosylated gp120 shielding gp41 (3, 4). Upon binding of gp120 to CD4 and a co-receptor (CCR5 or CXCR4), gp41 undergoes a large conformational change to form the prehairpin fusion intermediate in which the N-terminal and C-terminal helices separate from each other and the fusion peptide extends toward the host membrane (1, 5). This ultimately leads to the fusion of the viral and host membranes and leaves a postfusion form of gp41 with a structure of hairpins in a trimer.Several crystal structures of HIV-1 and simian immunodeficiency virus gp41 have been reported (6 -9). All structures contain the gp41 core, which is composed of the two heptad repeat regions, the N-terminal helical heptad repeat (HR1) and the C-terminal helical heptad repeat (HR2). The largest structur...